Strain identifier

BacDive ID: 8478

Type strain: Yes

Species: Mycobacterium doricum

Strain Designation: Fi-13295, ID 3931

Strain history: CIP <- 2001, E. Tortoli, Firenze, Italy: strain FI-13295 <- Piersimoni

NCBI tax ID(s): 126673 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 11685

BacDive-ID: 8478

DSM-Number: 44339

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, human pathogen

description: Mycobacterium doricum Fi-13295 is an aerobe, mesophilic human pathogen that was isolated from cerebrospinal fluid of an AIDS-patient.

NCBI tax id

  • NCBI tax id: 126673
  • Matching level: species

strain history

@refhistory
11685<- E. Tortoli, Coreggi Hospital, Fi-13295 <- Microbiol. Lab. Ancona
67770CIP 106867 <-- E. Tortoli FI-13295 <-- C. Piersimoni.
118966CIP <- 2001, E. Tortoli, Firenze, Italy: strain FI-13295 <- Piersimoni

doi: 10.13145/bacdive8478.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Mycobacteriaceae
  • genus: Mycobacterium
  • species: Mycobacterium doricum
  • full scientific name: Mycobacterium doricum Tortoli et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium doricum

@ref: 11685

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium doricum

full scientific name: Mycobacterium doricum Tortoli et al. 2001 emend. Nouioui et al. 2018

strain designation: Fi-13295, ID 3931

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.543
6948099.999positive
118966norod-shaped

colony morphology

  • @ref: 57161
  • incubation period: 10 days

multimedia

  • @ref: 11685
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44339.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11685LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)yeshttps://mediadive.dsmz.de/medium/354Name: LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354) Composition: Potato flour 18.6104 g/l L-Asparagin 2.23325 g/l KH2PO4 1.55087 g/l Mg-citrate 0.372208 g/l Malachite green 0.248139 g/l MgSO4 0.148883 g/l Glycerol Fresh egg mixture Distilled water
11685MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
33015MEDIUM 55 - for Mycobacteriumyes
118966CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
11685positivegrowth37mesophilic
33015positivegrowth37mesophilic
57161positivegrowth30-37mesophilic
67770positivegrowth37mesophilic
118966positivegrowth30-37mesophilic
118966nogrowth10psychrophilic
118966nogrowth22psychrophilic
118966nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57161aerobe
118966obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.965

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
118966606565hippurate-hydrolysis
11896617632nitrate+reduction
11896616301nitrite-reduction
11896617632nitrate-respiration

metabolite production

  • @ref: 118966
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118966oxidase-
118966beta-galactosidase-3.2.1.23
118966gelatinase-
118966amylase-
118966DNase-
118966catalase+1.11.1.6
118966tween esterase-
118966gamma-glutamyltransferase+2.3.2.2
118966lecithinase-
118966lipase-
118966protease-
118966urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118966-+++-+----++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118966--------------------------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
11685cerebrospinal fluid of an AIDS-patientAnconaItalyITAEurope
57161Human cerebrospinal fluidAnconaItalyITAEurope1995
67770Cerebrospinal fluid of an AIDS patientItalyITAEurope
118966Human, Cerebro-spinal fluidAnconaItalyITAEurope1995

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient
#Host Body Product#Fluids#Cerebrospinal fluid

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11685yes, in single cases1Risk group (German classification)
1189661Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium doricum strain DSM 44339 16S ribosomal RNA gene, partial sequenceAF547917542ena126673
11685Mycobacterium doricum 16S ribosomal RNA gene, partial sequenceAF2647001450ena126673

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium doricum JCM 12405GCA_010728155completencbi126673
66792Mycobacterium doricum strain DSM 44339126673.3wgspatric126673
66792Mycolicibacterium doricum strain JCM 12405126673.9completepatric126673
67770Mycolicibacterium doricum DSM 44339GCA_002102115contigncbi126673
66792Mycolicibacterium doricum CCUG 46352GCA_025822585scaffoldncbi126673

GC content

@refGC-contentmethod
6777066.5high performance liquid chromatography (HPLC)
6777067.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes61no
motileno94.374no
flagellatedno98.616no
gram-positiveyes87.334no
anaerobicno98.997yes
aerobicyes90.67yes
halophileno87.578no
spore-formingno87.993no
glucose-utilyes82.153no
thermophileno98.053yes
glucose-fermentno88.782no

External links

@ref: 11685

culture collection no.: DSM 44339, CIP 106867, CCUG 46352, JCM 12405, ATCC BAA 565

straininfo link

  • @ref: 77873
  • straininfo: 50579

literature

  • topic: Phylogeny
  • Pubmed-ID: 11760941
  • title: Mycobacterium doricum sp. nov.
  • authors: Tortoli E, Piersimoni C, Kroppenstedt RM, Montoya-Burgos JI, Reischl U, Giacometti A, Emler S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-6-2007
  • year: 2001
  • mesh: AIDS-Related Opportunistic Infections/*microbiology, Base Sequence, Cerebrospinal Fluid/*microbiology, DNA, Ribosomal/genetics, Fatty Acids/analysis, Humans, Male, Middle Aged, Molecular Sequence Data, Mycobacterium/chemistry/*classification/*genetics/isolation & purification, Mycobacterium Infections/*microbiology, Mycolic Acids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11685Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44339)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44339
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33015Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19045
57161Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46352)https://www.ccug.se/strain?id=46352
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
77873Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50579.1StrainInfo: A central database for resolving microbial strain identifiers
118966Curators of the CIPCollection of Institut Pasteur (CIP 106867)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106867